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<h1>Sirius Export</h1>

<h2>Description</h2>
<p>
    The module Export for Sirius exports spectral features for a selected peaklist or an aligned peaklist as .MGF format. 
    This .MGF file can be directly processed with Sirius (version 3.4 minimum). 
    Sirius uses both the deconvoluted isotopic pattern for each peak and the corresponding MS2 spectrum to rank molecular formula candidates. 
    Spectral features exported consist of a pair of MS1 and MS2 spectrum for each row. 
    Note that the MS1 spectrum can contain the deconvoluted isotopic peaks. 
    A masslist with mass detection performs on MS level 2 has to be generated first and selected.    
</p>

<h2>Instructions</h2>
<p>
    Before using the module, perform the following:
    <ol>        
        <li> Deconvolute isotopic peaks: 
            <br>- MZmine2 Menu: Peak list methods / Isotopes / Isotopic peaks grouper
        <li> Filter out peak without MS/MS spectrum associated. 
            <br>- MZmine2 Menu: Peak list methods / Filtering / Peak list row filter / Keep only peaks with MS2 scan (GNPS)
        <li> Reset the peak number ID.  
            <br>- MZmine2 Menu: Peak list methods / Filtering / Peak list row filter / Reset the peak number ID
        <li> Perform mass detection on MS level 2 and select. 
            <br>- MZmine2 Menu: Raw data methods / Mass detection 
            <br>[Make sure to use a noise threshold consistent with the MS level 2]
    </ol>
</p>

<h2>Documentation</h2>
<p>
    This module can be used in combination with the Export for GNPS module and imported back into GNPS molecular networks.
    Please refer to the following documentation for a detailed tutorial:
    <br>

    <ul>
        <li> Information about <a href="../../gnpsexport/help/help.html" target="_blank">GNPS export</a>
        <li> If you use the SIRIUS export module, cite <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395">MZmine2 paper</a>
             and the following article: <a href="http://dx.doi.org/10.1038/s41592-019-0344-8"> K. Dührkop, et al. “Sirius 4: a rapid tool for turning tandem mass spectra into metabolite structure information”, Nat methods, 2019.</a>
        <li> Sirius can be downloaded at the following address: <a href="https://bio.informatik.uni-jena.de/software/sirius/">https://bio.informatik.uni-jena.de/software/sirius/</a>
        <li> Sirius results can be mapped into <a href="http://gnps.ucsd.edu/">GNPS</a> molecular networks. <a href="https://bix-lab.ucsd.edu/display/Public/Mass+spectrometry+data+pre-processing+for+GNPS">See the documentation</a> here.
    </ul>
</p>
<!--
<h2>Parameters</h2>
<dl>
    <dt>FEATURE_ID</dt>
    <dd>Row number in the peak list</dd>

    <dt>PEPMASS</dt>
    <dd>Mass of the peak. If each row in the peak list contains several peaks (e.g. after performing alignment), the
        mass of the highest peak is chosen
    </dd>

    <dt>RTINSECONDS</dt>
    <dd>Retention time of the peak. If each row in the peak list contains several peaks, the average retention time
    is chosen</dd>

    <dt>SCANS</dt>
    <dd>The same as FEATURE_ID</dd>    

    <dt>CHARGE</dt>
    <dd>The charge for the specified row</dd>

    <dt>MSLEVEL</dt>
    <dd>Either equals 1 (MS) or 2 (MS/MS)</dd>
</dl>
-->
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